Zinc in PDB 8dc4: Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3

The structure of Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3, PDB code: 8dc4 was solved by K.Z.Guiley, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.37 / 2.40
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	68.56, 68.56, 220.212, 90, 90, 120
R / Rfree (%)	16.1 / 23.1

The binding sites of Zinc atom in the Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3 (pdb code 8dc4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3, PDB code: 8dc4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:39.6 occ:1.00 ND1 B:HIS179 1.9 36.2 1.0 SG B:CYS176 2.3 32.4 1.0 SG B:CYS238 2.3 30.6 1.0 SG B:CYS242 2.3 44.9 1.0 CE1 B:HIS179 2.6 22.5 1.0 CG B:HIS179 2.8 30.5 1.0 CB B:CYS242 3.3 43.7 1.0 CB B:CYS176 3.3 29.7 1.0 CB B:HIS179 3.4 30.7 1.0 NE2 B:HIS179 3.6 24.5 1.0 CB B:CYS238 3.7 42.5 1.0 CD2 B:HIS179 3.7 27.3 1.0 N B:CYS176 3.9 38.5 1.0 CA B:CYS176 4.2 34.5 1.0 N B:HIS179 4.2 41.2 1.0 CA B:CYS238 4.2 36.7 1.0 CA B:HIS179 4.4 32.2 1.0 CA B:CYS242 4.6 38.4 1.0 N B:TYR239 4.8 41.2 1.0 O B:CYS176 4.8 44.7 1.0 C B:CYS176 4.8 30.5 1.0 O B:MET237 5.0 25.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:38.8 occ:1.00 ND1 A:HIS179 1.8 16.9 1.0 CE1 A:HIS179 2.0 26.3 1.0 SG A:CYS242 2.3 24.9 1.0 SG A:CYS238 2.3 34.8 1.0 SG A:CYS176 2.3 37.8 1.0 CG A:HIS179 3.1 24.5 1.0 O A:HOH565 3.3 28.9 1.0 CB A:CYS242 3.3 32.3 1.0 NE2 A:HIS179 3.3 18.4 1.0 CB A:CYS176 3.4 29.3 1.0 CB A:CYS238 3.4 26.6 1.0 CA A:CYS238 3.8 26.3 1.0 CD2 A:HIS179 3.8 17.6 1.0 N A:CYS176 4.0 34.4 1.0 CB A:HIS179 4.0 29.8 1.0 N A:TYR239 4.2 22.8 1.0 CA A:CYS176 4.3 26.0 1.0 O A:HOH536 4.3 31.6 1.0 C A:CYS238 4.5 18.2 1.0 CA A:CYS242 4.7 40.5 1.0 O A:MET237 4.7 20.6 1.0 N A:HIS179 4.8 39.4 1.0 O A:CYS176 4.9 50.7 1.0 C A:CYS176 4.9 43.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:45.1 occ:1.00 ND1 C:HIS179 1.9 44.1 1.0 SG C:CYS242 2.3 50.0 1.0 SG C:CYS238 2.3 33.5 1.0 SG C:CYS176 2.3 29.5 1.0 CE1 C:HIS179 2.6 27.1 1.0 CG C:HIS179 2.9 28.4 1.0 CB C:CYS242 3.1 42.4 1.0 CB C:CYS176 3.5 22.0 1.0 CB C:HIS179 3.5 28.3 1.0 CB C:CYS238 3.6 52.8 1.0 NE2 C:HIS179 3.7 27.2 1.0 CD2 C:HIS179 3.9 24.6 1.0 N C:CYS176 4.1 43.9 1.0 CA C:CYS238 4.2 41.4 1.0 CA C:CYS176 4.3 32.3 1.0 N C:HIS179 4.4 39.3 1.0 CA C:CYS242 4.5 45.2 1.0 CA C:HIS179 4.6 32.0 1.0 N C:TYR239 4.7 42.7 1.0 O C:MET237 4.9 29.1 1.0 O C:CYS176 4.9 44.0 1.0 C C:CYS176 5.0 35.3 1.0 C C:CYS238 5.0 37.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of P53 Y220C Covalently Bound to Carbazole KG3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:33.2 occ:1.00 ND1 D:HIS179 1.8 25.7 1.0 SG D:CYS238 2.3 32.7 1.0 SG D:CYS242 2.3 34.2 1.0 SG D:CYS176 2.3 42.0 1.0 CE1 D:HIS179 2.4 30.8 1.0 CG D:HIS179 3.0 31.8 1.0 CB D:CYS242 3.3 40.4 1.0 CB D:CYS238 3.6 26.8 1.0 CB D:CYS176 3.6 24.9 1.0 NE2 D:HIS179 3.6 20.8 1.0 CB D:HIS179 3.8 33.0 1.0 CD2 D:HIS179 3.9 28.6 1.0 CA D:CYS238 4.0 25.6 1.0 N D:CYS176 4.1 31.3 1.0 N D:TYR239 4.4 27.9 1.0 CA D:CYS176 4.4 19.8 1.0 N D:HIS179 4.6 40.4 1.0 CA D:CYS242 4.7 40.6 1.0 C D:CYS238 4.7 19.7 1.0 O D:MET237 4.7 26.4 1.0 O D:CYS176 4.8 50.5 1.0 CA D:HIS179 4.8 39.8 1.0 C D:CYS176 5.0 43.8 1.0

K.Z.Guiley, K.M.Shokat. A Small Molecule Reacts with the P53 Somatic Mutant Y220C to Rescue Wild-Type Thermal Stability. Cancer Discov 2022.
ISSN: ESSN 2159-8290
PubMed: 36197521
DOI: 10.1158/2159-8290.CD-22-0381